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  Reaction coordinates and rates from transition paths

Best, R. B., & Hummer, G. (2005). Reaction coordinates and rates from transition paths. Proceedings of the National Academy of Sciences of the United States of America, 102(19), 6732-6737. doi:10.1073/pnas.0408098102.

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 Urheber:
Best, Robert B.1, Autor
Hummer, Gerhard1, Autor                 
Affiliations:
1Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, USA, ou_persistent22              

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Schlagwörter: Adenosine Triphosphate, Algorithms, Bayes Theorem, Biophysics, Hydrogen Bonding, Models, Molecular, Models, Statistical, Nanotechnology, Nanotubes, Carbon, Phase Transition, Probability, Protein Conformation, Protein Folding, Protein Structure, Secondary, Software, Water
 Zusammenfassung: The molecular mechanism of a reaction in solution is reflected in its transition-state ensemble and transition paths. We use a Bayesian formula relating the equilibrium and transition-path ensembles to identify transition states, rank reaction coordinates, and estimate rate coefficients. We also introduce a variational procedure to optimize reaction coordinates. The theory is illustrated with applications to protein folding and the dipole reorientation of an ordered water chain inside a carbon nanotube. To describe the folding of a simple model of a three-helix bundle protein, we variationally optimize the weights of a projection onto the matrix of native and nonnative amino acid contacts. The resulting one-dimensional reaction coordinate captures the folding transition state, with formation and packing of helix 2 and 3 constituting the bottleneck for folding.

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Sprache(n): eng - English
 Datum: 2004-10-312005-02-282005-05-10
 Publikationsstatus: Erschienen
 Seiten: 6
 Ort, Verlag, Ausgabe: -
 Inhaltsverzeichnis: -
 Art der Begutachtung: Expertenbegutachtung
 Identifikatoren: DOI: 10.1073/pnas.0408098102
BibTex Citekey: best_reaction_2005
 Art des Abschluß: -

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Titel: Proceedings of the National Academy of Sciences of the United States of America
Genre der Quelle: Zeitschrift
 Urheber:
Affiliations:
Ort, Verlag, Ausgabe: -
Seiten: - Band / Heft: 102 (19) Artikelnummer: - Start- / Endseite: 6732 - 6737 Identifikator: ISSN: 0027-8424